Hi martguys & Benoit, thanks for your quick feedback!
In my previous mail I thought you wanted whole genome pairwise alignments.
But what I have explained also apply to the homologues, you have to use the right formatter, which is in that case FASTAA
I had tried (weird guesswork) "set format=fastaa" in martshell.sh and that didn't work either. OK, let's forget about martshell. It seems martshell doesn't have an advantage over wget+XML-file. (BTW I wonder why martshell & company exist? Is it used by anyone? ) So...how can I set the formatter in the XML file? (not documented, the documentation says that the valid parameters could be found "elsewhere in this document".) I tried adding a "formatter" attribute with the value "fastaa"... that gives me : Query ERROR: caught BioMart::Exception: could not load module BioMart::Formatter::fastaa: Can't locate BioMart/Formatt er/fastaa.pm in @INC thanks again, cheers Max
